I read ebooks a lot in bed at night, very dark room (so my wife cannot sleep with any light on).

I found the lowest brightness setting of iPhone still gives quite bright in such dark room. I know most reader software have the option to have black background and white/yellow text; but I don't like it.

Which app are you using? I have the eReader app and the Stanza app, and both allow you to make significant, custom adjustments to the text/background colours. For instance, in Stanza I like the Old Parchment or Wood backgrounds - I find them much easier on the eyes. I note in eReader that you can select any colour in the palette from a colour wheel.

Are they the type of thing you're after, or have you used them and not found them useful?

I use eReader, Stanza, and Kindle on my iPhone. Even I lower the brightness to its lowest (either swipe down in Stanza, or brightness setting in Setting), it is still too bright in a totally dark room.

In version 1 of the iPhone OS, you could turn down the universal light setting so low that you couldn't see the slider to turn it up again (I had to try, of course ). They fixed that in version 2, but it's still quite low. Low enough for the OP; I think!